Gene expression lab, Instituto de Biomedicina de Sevilla
*September 2017 - October 2018*
Master's thesis student and research assistant
In the context of the master’s thesis (MSc in Molecular Genetics & Biotechnology), under the supervision of Dr. Sebastián Chávez de Diego and Dr. Gabriel Gutierrez Pozo and within Dr. Victoria Begley’s PhD project, I started studying Xrn1, a protein involved in the degradation of mRNA, and it’s role in the nucleosome localization and transcription in Saccharomyces cerevisiae. Using MNase-seq and following a DANPOS-based analysis, we found that the Xrn1 knockout mutant strains had higher nucleosome occupancy around TSS, which we related with a lower transcription initiation compared to WT strains, whereas in the gene body, the nucleosome occupancy was diminished as a consequence of RNA pol II backtracking. Results were validated using MNase-qPCR of two selected genes in Xrn1 conditional mutants.
My contributions to this research were:
- Bioinformatic analysis of the MNase-seq data.
- MNase-qPCR validation, including the yeast culture, the MNase-driven DNA digestion, the design of the primers and the following qPCRs.
Related publications:
- Begley et al (2020). Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration. RNA Biology. doi: 10.1080/15476286.2020.1845504{target="_blank"}.
Master’s thesis:
- Influence of Xrn1 in nucleosome positioning across Saccharomyces cerevisiae genome and its effects in transcription.